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Muthukrishnan V, Jaipurkar S, Damodaran N. Continuum topological derivative - a novel application tool for denoising CT and MRI medical images. BMC Med Imaging 2024; 24:182. [PMID: 39048968 PMCID: PMC11267933 DOI: 10.1186/s12880-024-01341-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/18/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND CT and MRI modalities are important diagnostics tools for exploring the anatomical and tissue properties, respectively of the human beings. Several advancements like HRCT, FLAIR and Propeller have advantages in diagnosing the diseases very accurately, but still have enough space for improvements due to the presence of inherent and instrument noises. In the case of CT and MRI, the quantum mottle and the Gaussian and Rayleigh noises, respectively are still present in their advanced modalities of imaging. This paper addresses the denoising problem with continuum topological derivative technique and proved its trustworthiness based on the comparative study with other traditional filtration methods such as spatial, adaptive, frequency and transformation techniques using measures like visual inspection and performance metrics. METHODS This research study focuses on identifying a novel method for denoising by testing different filters on HRCT (High-Resolution Computed Tomography) and MR (Magnetic Resonance) images. The images were acquired from the Image Art Radiological Scan Centre using the SOMATOM CT and SIGNA Explorer (operating at 1.5 Tesla) machines. To compare the performance of the proposed CTD (Continuum Topological Derivative) method, various filters were tested on both HRCT and MR images. The filters tested for comparison were Gaussian (2D convolution operator), Wiener (deconvolution operator), Laplacian and Laplacian diagonal (2nd order partial differential operator), Average, Minimum, and Median (ordinary spatial operators), PMAD (Anisotropic diffusion operator), Kuan (statistical operator), Frost (exponential convolution operator), and HAAR Wavelet (time-frequency operator). The purpose of the study was to evaluate the effectiveness of the CTD method in removing noise compared to the other filters. The performance metrics were analyzed to assess the diligence of noise removal achieved by the CTD method. The primary outcome of the study was the removal of quantum mottle noise in HRCT images, while the secondary outcome focused on removing Gaussian (foreground) and Rayleigh (background) noise in MR images. The study aimed to observe the dynamics of noise removal by examining the values of the performance metrics. In summary, this study aimed to assess the denoising ability of various filters in HRCT and MR images, with the CTD method being the proposed approach. The study evaluated the performance of each filter using specific metrics and compared the results to determine the effectiveness of the CTD method in removing noise from the images. RESULTS Based on the calculated performance metric values, it has been observed that the CTD method successfully removed quantum mottle noise in HRCT images and Gaussian as well as Rayleigh noise in MRI. This can be evidenced by the PSNR (Peak Signal-to-Noise Ratio) metric, which consistently exhibited values ranging from 50 to 65 for all the tested images. Additionally, the CTD method demonstrated remarkably low residual values, typically on the order of e-09, which is a distinctive characteristic across all the images. Furthermore, the performance metrics of the CTD method consistently outperformed those of the other tested methods. Consequently, the results of this study have significant implications for the quality, structural similarity, and contrast of HRCT and MR images, enabling clinicians to obtain finer details for diagnostic purposes. CONCLUSION Continuum topological derivative algorithm is found to be constructive in removing prominent noises in both CT and MRI images and can serve as a potential tool for recognition of anatomical details in case of diseased and normal ones. The results obtained from this research work are highly inspiring and offer great promise in obtaining accurate diagnostic information for critical cases such as Thoracic Cavity Carina, Brain SPI Globe Lens 4th Ventricle, Brain-Middle Cerebral Artery, Brain-Middle Cerebral Artery and neoplastic lesions. These findings lay the foundation for implementing the proposed CTD technique in routine clinical diagnosis.
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Affiliation(s)
- Viswanath Muthukrishnan
- Central Instrumentation & Service Laboratory, Guindy Campus, University of Madras, Chennai, India
| | | | - Nedumaran Damodaran
- Central Instrumentation & Service Laboratory, Guindy Campus, University of Madras, Chennai, India.
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Lee BWL, Chuah YH, Yoon J, Grinchuk OV, Liang Y, Hirpara JL, Shen Y, Wang LC, Lim YT, Zhao T, Sobota RM, Yeo TT, Wong ALA, Teo K, Nga VDW, Tan BWQ, Suda T, Toh TB, Pervaiz S, Lin Z, Ong DST. METTL8 links mt-tRNA m 3C modification to the HIF1α/RTK/Akt axis to sustain GBM stemness and tumorigenicity. Cell Death Dis 2024; 15:338. [PMID: 38744809 PMCID: PMC11093979 DOI: 10.1038/s41419-024-06718-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/02/2024] [Accepted: 05/02/2024] [Indexed: 05/16/2024]
Abstract
Epitranscriptomic RNA modifications are crucial for the maintenance of glioma stem cells (GSCs), the most malignant cells in glioblastoma (GBM). 3-methylcytosine (m3C) is a new epitranscriptomic mark on RNAs and METTL8 represents an m3C writer that is dysregulated in cancer. Although METTL8 has an established function in mitochondrial tRNA (mt-tRNA) m3C modification, alternative splicing of METTL8 can also generate isoforms that localize to the nucleolus where they may regulate R-loop formation. The molecular basis for METTL8 dysregulation in GBM, and which METTL8 isoform(s) may influence GBM cell fate and malignancy remain elusive. Here, we investigated the role of METTL8 in regulating GBM stemness and tumorigenicity. In GSC, METTL8 is exclusively localized to the mitochondrial matrix where it installs m3C on mt-tRNAThr/Ser(UCN) for mitochondrial translation and respiration. High expression of METTL8 in GBM is attributed to histone variant H2AZ-mediated chromatin accessibility of HIF1α and portends inferior glioma patient outcome. METTL8 depletion impairs the ability of GSC to self-renew and differentiate, thus retarding tumor growth in an intracranial GBM xenograft model. Interestingly, METTL8 depletion decreases protein levels of HIF1α, which serves as a transcription factor for several receptor tyrosine kinase (RTK) genes, in GSC. Accordingly, METTL8 loss inactivates the RTK/Akt axis leading to heightened sensitivity to Akt inhibitor treatment. These mechanistic findings, along with the intimate link between METTL8 levels and the HIF1α/RTK/Akt axis in glioma patients, guided us to propose a HIF1α/Akt inhibitor combination which potently compromises GSC proliferation/self-renewal in vitro. Thus, METTL8 represents a new GBM dependency that is therapeutically targetable.
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Affiliation(s)
- Bernice Woon Li Lee
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117593, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - You Heng Chuah
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117593, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jeehyun Yoon
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117593, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Oleg V Grinchuk
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117593, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yajing Liang
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117593, Singapore
| | - Jayshree L Hirpara
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Yating Shen
- The N.1 Institute for Health, National University of Singapore, Singapore, Singapore
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Loo Chien Wang
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yan Ting Lim
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Tianyun Zhao
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Radoslaw M Sobota
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Tseng Tsai Yeo
- Department of Surgery, Division of Neurosurgery, National University Hospital, Singapore, Singapore
| | - Andrea Li Ann Wong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- Department of Haematology-Oncology, National University Hospital, Singapore, Singapore
| | - Kejia Teo
- Department of Surgery, Division of Neurosurgery, National University Hospital, Singapore, Singapore
| | - Vincent Diong Weng Nga
- Department of Surgery, Division of Neurosurgery, National University Hospital, Singapore, Singapore
| | - Bryce Wei Quan Tan
- Department of Medicine, National University Hospital, Singapore, Singapore
| | - Toshio Suda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Tan Boon Toh
- The N.1 Institute for Health, National University of Singapore, Singapore, Singapore
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Shazib Pervaiz
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117593, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Zhewang Lin
- Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, 117543, Singapore, Singapore
| | - Derrick Sek Tong Ong
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117593, Singapore.
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
- National Neuroscience Institute, 308433, Singapore, Singapore.
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Liu J, Yang F, Hu J, Zhang X. Nanoparticles for efficient drug delivery and drug resistance in glioma: New perspectives. CNS Neurosci Ther 2024; 30:e14715. [PMID: 38708806 PMCID: PMC11071172 DOI: 10.1111/cns.14715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/24/2024] [Accepted: 03/27/2024] [Indexed: 05/07/2024] Open
Abstract
Gliomas are the most common primary tumors of the central nervous system, with glioblastoma multiforme (GBM) having the highest incidence, and their therapeutic efficacy depends primarily on the extent of surgical resection and the efficacy of postoperative chemotherapy. The role of the intracranial blood-brain barrier and the occurrence of the drug-resistant gene O6-methylguanine-DNA methyltransferase have greatly limited the efficacy of chemotherapeutic agents in patients with GBM and made it difficult to achieve the expected clinical response. In recent years, the rapid development of nanotechnology has brought new hope for the treatment of tumors. Nanoparticles (NPs) have shown great potential in tumor therapy due to their unique properties such as light, heat, electromagnetic effects, and passive targeting. Furthermore, NPs can effectively load chemotherapeutic drugs, significantly reduce the side effects of chemotherapeutic drugs, and improve chemotherapeutic efficacy, showing great potential in the chemotherapy of glioma. In this article, we reviewed the mechanisms of glioma drug resistance, the physicochemical properties of NPs, and recent advances in NPs in glioma chemotherapy resistance. We aimed to provide new perspectives on the clinical treatment of glioma.
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Affiliation(s)
- Jiyuan Liu
- Department of Neurosurgerythe First Hospital of China Medical UniversityShenyangChina
| | - Fan Yang
- Department of Cardiologythe Fourth Affiliated Hospital of China Medical UniversityShenyangChina
| | - Jinqu Hu
- Department of Neurosurgerythe First Hospital of China Medical UniversityShenyangChina
| | - Xiuchun Zhang
- Department of Neurologythe First Hospital of China Medical UniversityShenyangChina
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Cerneckis J, Ming GL, Song H, He C, Shi Y. The rise of epitranscriptomics: recent developments and future directions. Trends Pharmacol Sci 2024; 45:24-38. [PMID: 38103979 PMCID: PMC10843569 DOI: 10.1016/j.tips.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 12/19/2023]
Abstract
The epitranscriptomics field has undergone tremendous growth since the discovery that the RNA N6-methyladenosine (m6A) modification is reversible and is distributed throughout the transcriptome. Efforts to map RNA modifications transcriptome-wide and reshape the epitranscriptome in disease settings have facilitated mechanistic understanding and drug discovery in the field. In this review we discuss recent advancements in RNA modification detection methods and consider how these developments can be applied to gain novel insights into the epitranscriptome. We also highlight drug discovery efforts aimed at developing epitranscriptomic therapeutics for cancer and other diseases. Finally, we consider engineering of the epitranscriptome as an emerging direction to investigate RNA modifications and their causal effects on RNA processing at high specificity.
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Affiliation(s)
- Jonas Cerneckis
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Department of Cell and Developmental Biology, Department of Psychiatry, Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Department of Cell and Developmental Biology, the Epigenetics Institute, Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, the University of Chicago, Chicago, IL 60637, USA
| | - Yanhong Shi
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA.
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Li C, Li B, Wang H, Qu L, Liu H, Weng C, Han J, Li Y. Role of N6-methyladenosine methylation in glioma: recent insights and future directions. Cell Mol Biol Lett 2023; 28:103. [PMID: 38072944 PMCID: PMC10712162 DOI: 10.1186/s11658-023-00514-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Glioma is the most pervasive intracranial tumor in the central nervous system (CNS), with glioblastoma (GBM) being the most malignant type having a highly heterogeneous cancer cell population. There is a significantly high mortality rate in GBM patients. Molecular biomarkers related to GBM malignancy may have prognostic values in predicting survival outcomes and therapeutic responses, especially in patients with high-grade gliomas. In particular, N6-methyladenine (m6A) mRNA modification is the most abundant form of post-transcriptional RNA modification in mammals and is involved in regulating mRNA translation and degradation. Cumulative findings indicate that m6A methylation plays a crucial part in neurogenesis and glioma pathogenesis. In this review, we summarize recent advances regarding the functional significance of m6A modification and its regulatory factors in glioma occurrence and progression. Significant advancement of m6A methylation-associated regulators as potential therapeutic targets is also discussed.
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Affiliation(s)
- Chunlin Li
- Department of Neurology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250014, Shandong, China
| | - Bowen Li
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, 250000, Shandong, China
| | - Hui Wang
- Department of Acupuncture, Zaozhuang Traditional Chinese Medicine Hospital, Zaozhuang, 277000, Shandong, China
| | - Linglong Qu
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, 250000, Shandong, China
| | - Hui Liu
- First School of Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, 250000, Shandong, China
| | - Chao Weng
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Jinming Han
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China.
| | - Yuan Li
- Key Lab of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.
- Suzhou Research Institute of Shandong University, Suzhou 215123, China.
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Ramsoomair CK, Ceccarelli M, Heiss JD, Shah AH. The epitranscriptome of high-grade gliomas: a promising therapeutic target with implications from the tumor microenvironment to endogenous retroviruses. J Transl Med 2023; 21:893. [PMID: 38071304 PMCID: PMC10709919 DOI: 10.1186/s12967-023-04725-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
Glioblastoma (GBM) comprises 45.6% of all primary malignant brain cancers and is one of the most common and aggressive intracranial tumors in adults. Intratumoral heterogeneity with a wide range of proteomic, genetic, and epigenetic dysregulation contributes to treatment resistance and poor prognosis, thus demanding novel therapeutic approaches. To date, numerous clinical trials have been developed to target the proteome and epigenome of high-grade gliomas with promising results. However, studying RNA modifications, or RNA epitranscriptomics, is a new frontier within neuro-oncology. RNA epitranscriptomics was discovered in the 1970s, but in the last decade, the extent of modification of mRNA and various non-coding RNAs has emerged and been implicated in transposable element activation and many other oncogenic processes within the tumor microenvironment. This review provides background information and discusses the therapeutic potential of agents modulating epitranscriptomics in high-grade gliomas. A particular emphasis will be placed on how combination therapies that include immune agents targeting hERV-mediated viral mimicry could improve the treatment of GBM.
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Affiliation(s)
- Christian K Ramsoomair
- Section of Virology and Immunotherapy, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, 1095 NW 14Th Terrace, Miami, FL, 33136, USA.
- Medical Scientist Training Program, University of Miami Miller School of Medicine, 1095 NW 14Th Terrace, Miami, FL, 33136, USA.
| | - Michele Ceccarelli
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, 1550 N.W. 10Th Avenue, Miami, FL, 33136, USA
| | - John D Heiss
- Surgical Neurology Branch, Disorders and Stroke, National Institute of Neurological, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ashish H Shah
- Section of Virology and Immunotherapy, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, 1095 NW 14Th Terrace, Miami, FL, 33136, USA.
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